Table 1.
Number of GBM samples used in this study (downloaded from the TCGA repository on June 29, 2011, Sample IDs are in Table S1).
Figure 1.
PCA plot of GBM samples with methylation data.
Red: G-CIMP negative, Blue: G-CIMP positive. Methylation sites with std. deviation >0.2 are selected to generate this graph.
Figure 2.
Kaplan-Meier plot between old, young, and middle-aged GBM samples.
Table 2.
Number of differentially expressed genes between Old and Young GBM samples for three transcriptomic platforms.
Figure 3.
Genome-wide copy number alteration profiles of old and young GBM samples.
Data are from (a) Agilent Human Genome CGH Microarray 244A (Memorial Sloan-Kettering Cancer Center), (b) Affymetrix Genome-Wide Human SNP Array 6.0 (Broad Institute of MIT and Harvard), (c) Illumina 550 K Infinium HumanHap550 SNP Chip (HudsonAlpha Institute for Biotechnology) platforms (chr 1–23). Green bars represent amplification and red bars represent deletion. The height of each bar represents the frequency of the alteration in the group. The differentially amplified genes are in chromosome 7 and differentially deleted genes are in chromosome 10.
Table 3.
Number of mutated genes in old and young GNEG GBMs.
Figure 4.
Hierarchical clustering of GBM samples in the REMBRANDT and TCGA data sets.
(A) Clustering of old and young REMBRANDT GBM samples based on the expression profiles of age-specific genes derived from both TCGA Affymetrix U133A and Agilent G4502A data sets. (B) Clustering of old and young REMBRANDT GBM samples based on the expression profiles of all genes in the REMBRANDT data set. (C) Clustering of the old and young TCGA GBM samples based on the expression profiles of age-specific genes derived from both TCGA Affymetrix U133A and Agilent G4502A data sets.
Figure 5.
Source of variation of expression profiles of age-specific genes in the REMBRANDT data set.
The x-axis shows the components of the 3-way ANOVA model and the y-axis shows the median signal to noise ratio. The ANOVA model is built based on the expression profiles of the TCGA age-specific genes in REMBRANDT data set. The TCGA age-specific genes are the intersection of DEGs computed on TCGA Affymetrix U133A and Agilent G4502A data sets.
Figure 6.
Source of variation of expression profiles of all genes in the REMBRANDT data set.
The x-axis shows the components of the 3-way ANOVA model and the y-axis shows the median signal to noise ratio. The ANOVA model is built based on the expression profiles of all genes in REMBRANDT data set.
Figure 7.
IPA network of angiogenesis-related genes.
Node color represents the expression status based on Affymetrix U133A data set (Red: Upregulated in old GBMs, Green: Downregulated in old GBMs, Gray: Baseline, White: Unknown, Mix of green and red: both upregulated and downregulated genes in the complex).